@eagleoutice/flowr 1.3.14 → 1.4.1

package/r-bridge/lang-4.x/ast/model/processing/visitor.d.ts

@@ -1,4 +1,4 @@
-import { NoInfo, RNode } from '../model';
+import type { NoInfo, RNode } from '../model';
 /** Return `true` to stop visiting from this node (i.e., do not continue to visit this node *and* the children) */
 export type OnEnter<OtherInfo> = (node: RNode<OtherInfo>) => (boolean | void);
 /** Similar to {@link OnEnter} but called when leaving a node. Can't stop exploration as the subtree is already visited! */

package/r-bridge/lang-4.x/ast/parser/xml/config.d.ts

@@ -1,5 +1,5 @@
-import { MergeableRecord } from '../../../../../util/objects';
-import { TokenMap } from '../../../../retriever';
+import type { MergeableRecord } from '../../../../../util/objects';
+import type { TokenMap } from '../../../../retriever';
 /**
  * Configures the settings for the xml parser (like what names should be used to represent the given objects,
  * and what replacements are active with `xmlparsedata` on the R-side of things).

package/r-bridge/lang-4.x/ast/parser/xml/data.d.ts

@@ -1,8 +1,8 @@
-import { MergeableRecord } from '../../../../../util/objects';
-import { DeepReadonly } from 'ts-essentials';
-import { XmlParserConfig } from './config';
-import { XmlParserHooks } from './hooks';
-import { SourceRange } from '../../../../../util/range';
+import type { MergeableRecord } from '../../../../../util/objects';
+import type { DeepReadonly } from 'ts-essentials';
+import type { XmlParserConfig } from './config';
+import type { XmlParserHooks } from './hooks';
+import type { SourceRange } from '../../../../../util/range';
 /**
  * Contains all information populated and present during parsing and normalization of the R AST.
  */

package/r-bridge/lang-4.x/ast/parser/xml/hooks.d.ts

@@ -1,8 +1,8 @@
-import { NamedXmlBasedJson, XmlBasedJson } from './input-format';
-import { RNumber, NoInfo, RBinaryOp, RComment, RForLoop, RFunctionCall, RIfThenElse, RNode, RRepeatLoop, RString, RUnaryOp, RWhileLoop, RSymbol, RLogical, BinaryOperatorFlavor, RParameter, RFunctionDefinition, RArgument, UnaryOperatorFlavor, RBreak, RNext, RAccess, RLineDirective, RPipe } from '../../model';
-import { RNa } from '../../../values';
-import { ParserData } from './data';
-import { DeepReadonly, DeepRequired } from 'ts-essentials';
+import type { NamedXmlBasedJson, XmlBasedJson } from './input-format';
+import type { RNumber, NoInfo, RBinaryOp, RComment, RForLoop, RFunctionCall, RIfThenElse, RNode, RRepeatLoop, RString, RUnaryOp, RWhileLoop, RSymbol, RLogical, BinaryOperatorFlavor, RParameter, RFunctionDefinition, RArgument, UnaryOperatorFlavor, RBreak, RNext, RAccess, RLineDirective, RPipe } from '../../model';
+import type { RNa } from '../../../values';
+import type { ParserData } from './data';
+import type { DeepReadonly, DeepRequired } from 'ts-essentials';
 /** Denotes that if you return `undefined`, the parser will automatically take the original arguments (unchanged) */
 type AutoIfOmit<T> = T | undefined | void;
 /**

package/r-bridge/lang-4.x/ast/parser/xml/input-format.d.ts

@@ -1,4 +1,4 @@
-import { RawRType } from '../../model';
+import type { RawRType } from '../../model';
 /**
  * Thrown if the given input xml is not valid/contains unexpected elements.
  */

package/r-bridge/lang-4.x/ast/parser/xml/internal/access.d.ts

@@ -1,6 +1,6 @@
-import { NamedXmlBasedJson } from '../input-format';
-import { ParserData } from '../data';
-import { RAccess } from '../../../model';
+import type { NamedXmlBasedJson } from '../input-format';
+import type { ParserData } from '../data';
+import type { RAccess } from '../../../model';
 /**
  * Tries to normalize the given data as access (e.g., indexing).
  *

package/r-bridge/lang-4.x/ast/parser/xml/internal/control/if-then-else.d.ts

@@ -1,6 +1,6 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RIfThenElse } from '../../../../model';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RIfThenElse } from '../../../../model';
 /**
  * Try to parse the construct as a {@link RIfThenElse}.
  */

package/r-bridge/lang-4.x/ast/parser/xml/internal/control/if-then.d.ts

@@ -1,6 +1,6 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RIfThenElse } from '../../../../model';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RIfThenElse } from '../../../../model';
 /**
  * Try to parse the construct as a {@link RIfThenElse}.
  */

package/r-bridge/lang-4.x/ast/parser/xml/internal/expression/expression.d.ts

@@ -1,6 +1,6 @@
-import { XmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RNode } from '../../../../model';
+import type { XmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RNode } from '../../../../model';
 /**
  * Returns an expression list if there are multiple children, otherwise returns the single child directly with no expr wrapper
  *

package/r-bridge/lang-4.x/ast/parser/xml/internal/functions/argument.d.ts

@@ -1,6 +1,6 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { RArgument } from '../../../../model';
-import { ParserData } from '../../data';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { RArgument } from '../../../../model';
+import type { ParserData } from '../../data';
 /**
  * Either parses `[expr]` or `[SYMBOL_SUB, EQ_SUB, expr]` as an argument of a function call in R.
  * Probably directly called by the function call parser as otherwise, we do not expect to find arguments.

package/r-bridge/lang-4.x/ast/parser/xml/internal/functions/call.d.ts

@@ -1,6 +1,6 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RFunctionCall, RNext, RBreak } from '../../../../model';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RFunctionCall, RNext, RBreak } from '../../../../model';
 /**
  * Tries to parse the given data as a function call.
  *

package/r-bridge/lang-4.x/ast/parser/xml/internal/functions/definition.d.ts

@@ -1,6 +1,6 @@
-import { ParserData } from '../../data';
-import { NamedXmlBasedJson } from '../../input-format';
-import { RFunctionDefinition } from '../../../../model';
+import type { ParserData } from '../../data';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { RFunctionDefinition } from '../../../../model';
 /**
  * Tries to parse the given data as a function definition.
  *

package/r-bridge/lang-4.x/ast/parser/xml/internal/functions/parameter.d.ts

@@ -1,6 +1,6 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { RParameter } from '../../../../model';
-import { ParserData } from '../../data';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { RParameter } from '../../../../model';
+import type { ParserData } from '../../data';
 /**
  * Either parses `[SYMBOL_FORMALS]` or `[SYMBOL_FORMALS, EQ_FORMALS, expr]` as a parameter of a function definition in R.
  * Probably directly called by the function definition parser as otherwise, we do not expect to find parameters.

package/r-bridge/lang-4.x/ast/parser/xml/internal/loops/break.d.ts

@@ -1,4 +1,4 @@
-import { ParserData } from '../../data';
-import { XmlBasedJson } from '../../input-format';
-import { RBreak } from '../../../../model';
+import type { ParserData } from '../../data';
+import type { XmlBasedJson } from '../../input-format';
+import type { RBreak } from '../../../../model';
 export declare function normalizeBreak(data: ParserData, obj: XmlBasedJson): RBreak;

package/r-bridge/lang-4.x/ast/parser/xml/internal/loops/for.d.ts

@@ -1,4 +1,4 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RForLoop } from '../../../../model';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RForLoop } from '../../../../model';
 export declare function tryNormalizeFor(data: ParserData, forToken: NamedXmlBasedJson, head: NamedXmlBasedJson, body: NamedXmlBasedJson): RForLoop | undefined;

package/r-bridge/lang-4.x/ast/parser/xml/internal/loops/next.d.ts

@@ -1,4 +1,4 @@
-import { ParserData } from '../../data';
-import { XmlBasedJson } from '../../input-format';
-import { RNext } from '../../../../model';
+import type { ParserData } from '../../data';
+import type { XmlBasedJson } from '../../input-format';
+import type { RNext } from '../../../../model';
 export declare function normalizeNext(data: ParserData, obj: XmlBasedJson): RNext;

package/r-bridge/lang-4.x/ast/parser/xml/internal/loops/repeat.d.ts

@@ -1,6 +1,6 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RRepeatLoop } from '../../../../model';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RRepeatLoop } from '../../../../model';
 /**
  * Try to parse the construct as a {@link RRepeatLoop}.
  *

package/r-bridge/lang-4.x/ast/parser/xml/internal/loops/while.d.ts

@@ -1,4 +1,4 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RWhileLoop } from '../../../../model';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RWhileLoop } from '../../../../model';
 export declare function tryNormalizeWhile(data: ParserData, whileToken: NamedXmlBasedJson, leftParen: NamedXmlBasedJson, condition: NamedXmlBasedJson, rightParen: NamedXmlBasedJson, body: NamedXmlBasedJson): RWhileLoop | undefined;

package/r-bridge/lang-4.x/ast/parser/xml/internal/meta.d.ts

@@ -1,7 +1,7 @@
-import { NamedXmlBasedJson, XmlBasedJson } from '../input-format';
-import { SourceRange } from '../../../../../../util/range';
-import { XmlParserConfig } from '../config';
-import { RawRType, RExpressionList, RNode } from '../../../model';
+import type { NamedXmlBasedJson, XmlBasedJson } from '../input-format';
+import type { SourceRange } from '../../../../../../util/range';
+import type { XmlParserConfig } from '../config';
+import type { RawRType, RExpressionList, RNode } from '../../../model';
 /**
  * if the passed object is an array with only one element, remove the array wrapper
  */

package/r-bridge/lang-4.x/ast/parser/xml/internal/operators/binary.d.ts

@@ -1,6 +1,6 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RNode } from '../../../../model';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RNode } from '../../../../model';
 /**
  * Parsing binary operations includes the pipe, even though the produced PIPE construct is not a binary operation,
  * to ensure it is handled separately from the others (especially in the combination of a pipe bind)

package/r-bridge/lang-4.x/ast/parser/xml/internal/operators/special.d.ts

@@ -1,4 +1,4 @@
-import { BinaryOperatorFlavor } from '../../../../model';
+import type { BinaryOperatorFlavor } from '../../../../model';
 /**
  * Identify the flavor of a given operator, as we do not really have a use for "special"
  * operators within our internal AST.

package/r-bridge/lang-4.x/ast/parser/xml/internal/operators/unary.d.ts

@@ -1,6 +1,6 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RNode } from '../../../../model';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RNode } from '../../../../model';
 /**
  * Parses the construct as a {@link RUnaryOp} (automatically identifies the flavor).
  *

package/r-bridge/lang-4.x/ast/parser/xml/internal/other/comment.d.ts

@@ -1,6 +1,6 @@
-import { XmlBasedJson } from '../../input-format';
-import { RComment } from '../../../../model';
-import { ParserData } from '../../data';
+import type { XmlBasedJson } from '../../input-format';
+import type { RComment } from '../../../../model';
+import type { ParserData } from '../../data';
 /**
  * Normalize the given object as an R comment.
  * This requires you to check the corresponding name beforehand.

package/r-bridge/lang-4.x/ast/parser/xml/internal/other/line-directive.d.ts

@@ -1,6 +1,6 @@
-import { XmlBasedJson } from '../../input-format';
-import { RComment, RLineDirective } from '../../../../model';
-import { ParserData } from '../../data';
+import type { XmlBasedJson } from '../../input-format';
+import type { RComment, RLineDirective } from '../../../../model';
+import type { ParserData } from '../../data';
 /**
  * Normalize the given object as an R line directive (`#line <number> "<file>"`).
  * This requires you to check the corresponding name beforehand.

package/r-bridge/lang-4.x/ast/parser/xml/internal/structure/elements.d.ts

@@ -1,7 +1,7 @@
-import { NamedXmlBasedJson, XmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RNode } from '../../../../model';
-import { RDelimiter } from '../../../../model/nodes/info';
+import type { NamedXmlBasedJson, XmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RNode } from '../../../../model';
+import type { RDelimiter } from '../../../../model/nodes/info';
 export declare function splitComments(mappedWithName: NamedXmlBasedJson[]): {
     comments: NamedXmlBasedJson[];
     others: NamedXmlBasedJson[];

package/r-bridge/lang-4.x/ast/parser/xml/internal/structure/root.d.ts

@@ -1,4 +1,4 @@
-import { XmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RExpressionList } from '../../../../model';
+import type { XmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RExpressionList } from '../../../../model';
 export declare function parseRootObjToAst(data: ParserData, obj: XmlBasedJson): RExpressionList;

package/r-bridge/lang-4.x/ast/parser/xml/internal/structure/single-element.d.ts

@@ -1,7 +1,7 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { ParserData } from '../../data';
-import { RNode } from '../../../../model';
-import { RDelimiter } from '../../../../model/nodes/info';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { ParserData } from '../../data';
+import type { RNode } from '../../../../model';
+import type { RDelimiter } from '../../../../model/nodes/info';
 /**
  * Parses a single structure in the ast based on its type (e.g., a string, a number, a symbol, ...)
  *

package/r-bridge/lang-4.x/ast/parser/xml/internal/values/number.d.ts

@@ -1,7 +1,7 @@
-import { XmlBasedJson } from '../../input-format';
-import { RNa } from '../../../../../values';
-import { RLogical, RSymbol, NoInfo, RNumber } from '../../../../model';
-import { ParserData } from '../../data';
+import type { XmlBasedJson } from '../../input-format';
+import type { RNa } from '../../../../../values';
+import type { RLogical, RSymbol, NoInfo, RNumber } from '../../../../model';
+import type { ParserData } from '../../data';
 /**
  * Normalize the given object as a R number (see {@link number2ts}), supporting booleans (see {@link boolean2ts}),
  * and special values.

package/r-bridge/lang-4.x/ast/parser/xml/internal/values/string.d.ts

@@ -1,6 +1,6 @@
-import { XmlBasedJson } from '../../input-format';
-import { RString } from '../../../../model';
-import { ParserData } from '../../data';
+import type { XmlBasedJson } from '../../input-format';
+import type { RString } from '../../../../model';
+import type { ParserData } from '../../data';
 /**
  * Normalize the given object as a R string (see {@link string2ts}).
  * This requires you to check the corresponding name beforehand.

package/r-bridge/lang-4.x/ast/parser/xml/internal/values/symbol.d.ts

@@ -1,6 +1,6 @@
-import { NamedXmlBasedJson } from '../../input-format';
-import { RSymbol } from '../../../../model';
-import { ParserData } from '../../data';
+import type { NamedXmlBasedJson } from '../../input-format';
+import type { RSymbol } from '../../../../model';
+import type { ParserData } from '../../data';
 /**
  * Normalize the given object as an R symbol (incorporating namespace information).
  * <p>

package/r-bridge/lang-4.x/ast/parser/xml/internal/xml-to-json.d.ts

@@ -1,5 +1,5 @@
-import { XmlParserConfig } from '../config';
-import { XmlBasedJson } from '../input-format';
+import type { XmlParserConfig } from '../config';
+import type { XmlBasedJson } from '../input-format';
 /**
  * Parse the xml presented by R into a json object that will be used for conversion
  *

package/r-bridge/lang-4.x/ast/parser/xml/parser.d.ts

@@ -1,7 +1,7 @@
-import { NormalizedAst, IdGenerator, NoInfo } from '../../model';
-import { XmlParserHooks } from './hooks';
-import { DeepPartial } from 'ts-essentials';
-import { TokenMap } from '../../../../retriever';
+import type { NormalizedAst, IdGenerator, NoInfo } from '../../model';
+import type { XmlParserHooks } from './hooks';
+import type { DeepPartial } from 'ts-essentials';
+import type { TokenMap } from '../../../../retriever';
 export declare const parseLog: import("tslog").Logger<import("tslog").ILogObj>;
 /**
  * The main entry point to normalize the given R ast.

package/r-bridge/retriever.d.ts

@@ -1,6 +1,6 @@
 import { type RShell } from './shell';
-import { XmlParserHooks, NormalizedAst } from './lang-4.x';
-import { DeepPartial, DeepReadonly } from 'ts-essentials';
+import type { XmlParserHooks, NormalizedAst } from './lang-4.x';
+import type { DeepPartial, DeepReadonly } from 'ts-essentials';
 export interface RParseRequestFromFile {
     request: 'file';
     /** The path to the file (absolute paths are probably best here */

package/r-bridge/shell-executor.d.ts

@@ -0,0 +1,25 @@
+import type { RShellExecutionOptions } from './shell';
+import type { SemVer } from 'semver';
+import type { TokenMap } from './retriever';
+export declare class RShellExecutor {
+    readonly options: Readonly<RShellExecutionOptions>;
+    private readonly log;
+    private readonly prerequisites;
+    constructor(options?: Partial<RShellExecutionOptions>);
+    continueOnError(): RShellExecutor;
+    injectLibPaths(...paths: string[]): RShellExecutor;
+    tryToInjectHomeLibPath(): RShellExecutor;
+    addPrerequisites(commands: string | string[]): RShellExecutor;
+    usedRVersion(): SemVer | null;
+    allInstalledPackages(): string[];
+    isPackageInstalled(packageName: string): boolean;
+    ensurePackageInstalled(packageName: string, autoload?: boolean, force?: boolean): {
+        packageName: string;
+        packageExistedAlready: boolean;
+        /** the temporary directory used for the installation, undefined if none was used */
+        libraryLocation?: string;
+    };
+    obtainTempDir(): string;
+    getTokenMap(): TokenMap;
+    run(commands: string | string[], returnErr?: boolean): string;
+}

package/r-bridge/shell-executor.js

@@ -0,0 +1,119 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RShellExecutor = void 0;
+const shell_1 = require("./shell");
+const objects_1 = require("../util/objects");
+const child_process_1 = require("child_process");
+const lang_4_x_1 = require("./lang-4.x");
+const preload_1 = __importDefault(require("semver/preload"));
+const log_1 = require("../util/log");
+const fs_1 = __importDefault(require("fs"));
+const retriever_1 = require("./retriever");
+class RShellExecutor {
+    options;
+    log;
+    prerequisites = [];
+    constructor(options) {
+        this.options = (0, objects_1.deepMergeObject)(shell_1.DEFAULT_R_SHELL_OPTIONS, options);
+        this.log = log_1.log.getSubLogger({ name: 'RShellExecutor' });
+    }
+    continueOnError() {
+        this.log.info('continue in case of Errors');
+        this.addPrerequisites('options(error=function() {})');
+        return this;
+    }
+    injectLibPaths(...paths) {
+        this.log.debug(`injecting lib paths ${JSON.stringify(paths)}`);
+        this.addPrerequisites(`.libPaths(c(.libPaths(), ${paths.map(lang_4_x_1.ts2r).join(',')}))`);
+        return this;
+    }
+    tryToInjectHomeLibPath() {
+        if (this.options.homeLibPath === undefined) {
+            this.log.debug('ensuring home lib path exists (automatic inject)');
+            this.addPrerequisites([
+                'if(!dir.exists(Sys.getenv("R_LIBS_USER"))) { dir.create(path=Sys.getenv("R_LIBS_USER"),showWarnings=FALSE,recursive=TRUE) }',
+                '.libPaths(c(.libPaths(), Sys.getenv("R_LIBS_USER")))'
+            ]);
+        }
+        else {
+            this.injectLibPaths(this.options.homeLibPath);
+        }
+        return this;
+    }
+    addPrerequisites(commands) {
+        this.prerequisites.push(...(typeof commands == 'string' ? [commands] : commands));
+        return this;
+    }
+    usedRVersion() {
+        const version = this.run(`cat(paste0(R.version$major,".",R.version$minor), ${(0, lang_4_x_1.ts2r)(this.options.eol)})`);
+        this.log.trace(`raw version: ${JSON.stringify(version)}`);
+        return preload_1.default.coerce(version);
+    }
+    allInstalledPackages() {
+        this.log.debug('getting all installed packages');
+        const packages = this.run(`cat(paste0(installed.packages()[,1], collapse=","),"${this.options.eol}")`);
+        return packages.split(',');
+    }
+    isPackageInstalled(packageName) {
+        this.log.debug(`checking if package "${packageName}" is installed`);
+        return this.run(`cat(system.file(package="${packageName}")!="","${this.options.eol}")`) === 'TRUE';
+    }
+    ensurePackageInstalled(packageName, autoload = false, force = false) {
+        const packageExistedAlready = this.isPackageInstalled(packageName);
+        if (!force && packageExistedAlready) {
+            this.log.info(`package "${packageName}" is already installed`);
+            if (autoload)
+                this.addPrerequisites(`library(${(0, lang_4_x_1.ts2r)(packageName)})`);
+            return { packageName, packageExistedAlready };
+        }
+        const tempDir = this.obtainTempDir();
+        this.log.debug(`using temporary directory: "${tempDir}" to install package "${packageName}"`);
+        this.run(`install.packages(${(0, lang_4_x_1.ts2r)(packageName)},repos="https://cloud.r-project.org/",quiet=FALSE,lib=temp)`);
+        if (autoload)
+            this.addPrerequisites(`library(${(0, lang_4_x_1.ts2r)(packageName)},lib.loc=temp)`);
+        return { packageName, packageExistedAlready, libraryLocation: tempDir };
+    }
+    obtainTempDir() {
+        const tempDir = this.run([
+            'temp <- tempdir()',
+            `cat(temp, ${(0, lang_4_x_1.ts2r)(this.options.eol)})`
+        ]);
+        log_1.log.info(`obtained temp dir ${tempDir}`);
+        const deleteOnExit = function () {
+            if (fs_1.default.existsSync(tempDir)) {
+                log_1.log.info(`deleting temp dir ${tempDir}`);
+                fs_1.default.rmSync(tempDir, { recursive: true, force: true });
+            }
+        };
+        process.on('SIGINT', deleteOnExit);
+        process.on('SIGTERM', deleteOnExit);
+        return tempDir;
+    }
+    getTokenMap() {
+        this.ensurePackageInstalled('xmlparsedata', true);
+        // we invert the token map to get a mapping back from the replacement
+        const parsed = (0, lang_4_x_1.parseCSV)(this.run('write.table(xmlparsedata::xml_parse_token_map,sep=",",col.names=FALSE)').split('\n'));
+        if (parsed.some(s => s.length !== 2))
+            throw new Error(`Expected two columns in token map, but got ${JSON.stringify(parsed)}`);
+        // we swap key and value to get the other direction, furthermore we remove quotes from keys if they are quoted
+        const ret = {};
+        for (const [key, value] of parsed)
+            ret[value] = (0, retriever_1.removeTokenMapQuotationMarks)(key);
+        return ret;
+    }
+    run(commands, returnErr = false) {
+        this.log.trace(`> ${JSON.stringify(commands)}`);
+        const returns = (0, child_process_1.spawnSync)(this.options.pathToRExecutable, this.options.commandLineOptions, {
+            env: this.options.env,
+            cwd: this.options.cwd,
+            encoding: 'utf8',
+            input: [...this.prerequisites, commands].join(this.options.eol)
+        });
+        return (returnErr ? returns.stderr : returns.stdout).trim();
+    }
+}
+exports.RShellExecutor = RShellExecutor;
+//# sourceMappingURL=shell-executor.js.map

package/r-bridge/shell.d.ts

@@ -1,7 +1,7 @@
 /// <reference types="node" />
 import { type MergeableRecord } from '../util/objects';
-import { SemVer } from 'semver';
-import { TokenMap } from './retriever';
+import type { SemVer } from 'semver';
+import type { TokenMap } from './retriever';
 export type OutputStreamSelector = 'stdout' | 'stderr' | 'both';
 export interface CollectorTimeout extends MergeableRecord {
     /**
@@ -33,7 +33,7 @@ export interface OutputCollectorConfiguration extends MergeableRecord {
     automaticallyTrimOutput: boolean;
 }
 export declare const DEFAULT_OUTPUT_COLLECTOR_CONFIGURATION: OutputCollectorConfiguration;
-export interface RShellSessionOptions extends MergeableRecord {
+export interface RShellExecutionOptions extends MergeableRecord {
     /** The path to the R executable, can be only the executable if it is to be found on the PATH. */
     readonly pathToRExecutable: string;
     /** Command line options to use when starting the R session. */
@@ -44,12 +44,14 @@ export interface RShellSessionOptions extends MergeableRecord {
     readonly eol: string;
     /** The environment variables available in the R session. */
     readonly env: NodeJS.ProcessEnv;
+    /** The path to the library directory, use undefined to let R figure that out for itself */
+    readonly homeLibPath: string | undefined;
+}
+export interface RShellSessionOptions extends RShellExecutionOptions {
     /** If set, the R session will be restarted if it exits due to an error */
     readonly revive: 'never' | 'on-error' | 'always';
     /** Called when the R session is restarted, this makes only sense if `revive` is not set to `'never'` */
     readonly onRevive: (code: number, signal: string | null) => void;
-    /** The path to the library directory, use undefined to let R figure that out for itself */
-    readonly homeLibPath: string | undefined;
 }
 /**
  * Configuration of an {@link RShell} instance.
@@ -58,6 +60,7 @@ export interface RShellSessionOptions extends MergeableRecord {
 export interface RShellOptions extends RShellSessionOptions {
     readonly sessionName: string;
 }
+export declare const DEFAULT_R_SHELL_EXEC_OPTIONS: RShellExecutionOptions;
 export declare const DEFAULT_R_SHELL_OPTIONS: RShellOptions;
 /**
  * The `RShell` represents an interactive session with the R interpreter.

package/r-bridge/shell.js

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.RShell = exports.DEFAULT_R_SHELL_OPTIONS = exports.DEFAULT_OUTPUT_COLLECTOR_CONFIGURATION = void 0;
+exports.RShell = exports.DEFAULT_R_SHELL_OPTIONS = exports.DEFAULT_R_SHELL_EXEC_OPTIONS = exports.DEFAULT_OUTPUT_COLLECTOR_CONFIGURATION = void 0;
 const child_process_1 = require("child_process");
 const objects_1 = require("../util/objects");
 const readline = __importStar(require("node:readline"));
@@ -47,14 +47,17 @@ exports.DEFAULT_OUTPUT_COLLECTOR_CONFIGURATION = {
     automaticallyTrimOutput: true,
     errorStopsWaiting: true
 };
-exports.DEFAULT_R_SHELL_OPTIONS = {
-    sessionName: 'default',
+exports.DEFAULT_R_SHELL_EXEC_OPTIONS = {
     pathToRExecutable: (0, os_1.getPlatform)() === 'windows' ? 'R.exe' : 'R',
     commandLineOptions: ['--vanilla', '--quiet', '--no-echo', '--no-save'],
     cwd: process.cwd(),
     env: process.env,
     eol: '\n',
     homeLibPath: (0, os_1.getPlatform)() === 'windows' ? undefined : '~/.r-libs',
+};
+exports.DEFAULT_R_SHELL_OPTIONS = {
+    ...exports.DEFAULT_R_SHELL_EXEC_OPTIONS,
+    sessionName: 'default',
     revive: 'never',
     onRevive: () => { }
 };

package/reconstruct/reconstruct.d.ts

@@ -3,7 +3,7 @@
  * as the file itself is way too long). See {@link reconstructToCode}.
  * @module
  */
-import { NormalizedAst, NodeId, ParentInformation, RNode } from '../r-bridge';
+import type { NormalizedAst, NodeId, ParentInformation, RNode } from '../r-bridge';
 type Selection = Set<NodeId>;
 export declare const reconstructLogger: import("tslog").Logger<import("tslog").ILogObj>;
 /** The structure of the predicate that should be used to determine if a given normalized node should be included in the reconstructed code independent of if it is selected by the slice or not */

package/slicing/criterion/collect-all.d.ts

@@ -3,9 +3,9 @@
  * This module provides a function to collect all slicing criteria.
  * @module
  */
-import { MergeableRecord } from '../../util/objects';
-import { NodeId, RNodeWithParent } from '../../r-bridge';
-import { SlicingCriteria } from './parse';
+import type { MergeableRecord } from '../../util/objects';
+import type { NodeId, RNodeWithParent } from '../../r-bridge';
+import type { SlicingCriteria } from './parse';
 /**
  * Defines the filter for collecting all possible slicing criteria.
  * @see DefaultAllVariablesFilter

package/slicing/criterion/filters/all-variables.d.ts

@@ -1,2 +1,2 @@
-import { SlicingCriteriaFilter } from '../collect-all';
+import type { SlicingCriteriaFilter } from '../collect-all';
 export declare const DefaultAllVariablesFilter: SlicingCriteriaFilter;

package/slicing/criterion/parse.d.ts

@@ -1,4 +1,4 @@
-import { NormalizedAst, NodeId, NoInfo, ParentInformation } from '../../r-bridge';
+import type { NormalizedAst, NodeId, NoInfo, ParentInformation } from '../../r-bridge';
 /** Either `line:column`, `line@variable-name`, or `$id` */
 export type SingleSlicingCriterion = `${number}:${number}` | `${number}@${string}` | `$${number}`;
 export type SlicingCriteria = SingleSlicingCriterion[];